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RNA-Seq: iReckon: Simultaneous isoform discovery and abundance estimation from RNA-se Newsbot! Literature Watch 0 12-04-2012 02:00 AM

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Old 02-26-2013, 08:07 AM   #1
acervera
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Location: Helsinki

Join Date: Feb 2012
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Wink has anyone tried iReckon?

Hi,
I want to try iReckon on my RNA-Seq data, but I haven't succeeded in getting the correct format for the reference and annotation files.
Has anyone tried it?
I tried formatting my genome.fa with Savant, but I could not find how to format a fasta file there. Also, I would like to use an annotation file from Ensembl and not UCSC, but after converting my gtf to bed format it was not accepted by iReckon.

I tried the following comand:

java -Xmx15000M -jar IReckon-1.0.6.jar accepted_hits.bam genome.fa genes.bed -1 reads.fa

Any help will be very much appreciated!
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